鲤鱼同源框基因家族HoxA2b基因生物信息学分析

Bioinformatics analysis on common carp Homeobox A2b gene

Hox基因家族是一组决定胚胎发育的关键基因,也是研究生物进化中染色体加倍和基因复制的重要模型之一。通过利用比较基因组学和生物信息学的方法,对鲤鱼基因组数据库的HoxA2b基因进行调取、序列分析比较,绘制4种同源进化树,结果发现:HoxA2b基因十分保守,大多数鲤科鱼类HoxA2b基因同源性在99%～100%;找到一段所有生物共有的保守序列,长度为188 bp,编码62个氨基酸;鲤鱼的HoxA2b基因与其他20种生物的保守区同源性在85%～100%,相对遗传距离在1.14～1.55之间;对碱基替代率进行分析发现非同义碱基替代率远远高于同义碱基替代率,认为鲤鱼的HoxA2b基因变异较大,与其他生物的HoxA2b基因遗传距离较远,可能与鲤鱼的基因组复制和染色体加倍有关。

Hox gene family is a set of key genes of embryo development and one of the important models to study gene duplication and chromosome doubling during biological evolution. In this paper, by using comparative genomics and bioinformatics approach, we extracted HoxA2b gene sequence from the carp genome database and accomplished sequence analysis and comparison, and drew four kinds of homologous evolutionary tree. As a result, it is found that HoxA2b gene is very conservative and the homology of most of Cyprinidae HoxA2b genes is between 99% - 100%. We found a conserved sequence whose length is 188 bp, encoding 62 amino acids. The homology in the conserved region of carp HoxA2b gene with other 20 organisms is about 85% - 100% and the relative genetic distance is between 1.14 - 1.55. By analysis the rate of base substitution, we found that the non-synonymous nucleotide substitution rate is much higher than synonymous nucleotide substitution rate. The carp HoxA2b gene has greater genetic variation and has far genetic distance with other organisms which may be related to carp genome replication and chromosome doubling.